To the title question: yes, certainly. You will have to provide transcripts from all institutions attended. Every institution will have its own procedure for "converting" your transcripts into something that allows candidates to be compared apples-to-apples. While these procedures will vary widely, it would be strange to consider only those classes taken at your home institution. After all, some students specifically take classes at other universities to strengthen their profiles when applying to graduate school.
The key point in your case, however, is that these are "gen eds" (general education classes). Regardless of where these classes were taken, they likely have little bearing on your suitability for graduate study. Even less so if these poor grades are older than your good grades. So you probably have nothing to worry about.
In fact, there is probably no need to comment on or explain these poor grades at all in your application. Your "amazing" transcript speaks for itself. However, if there is a compelling reason for the anomaly that you wish to explain, you may do so if you can do it in one sentence. For example: "I completed my general education requirements while studying abroad in Essos, but as I did not speak Dothraki, my grades that semester were a bit of an anomaly."